Evangelia Kalligiannaki

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In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general(More)
We propose a hierarchy of two-level kinetic Monte Carlo methods for sampling highdimensional, stochastic lattice particle dynamics with complex interactions. The method is based on the efficient coupling of different spatial resolution levels, taking advantage of the low sampling cost in a coarse space and developing local reconstruction strategies from(More)
Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to(More)
In this work we propose a hierarchy of Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each Monte Carlo step is composed by two or more sub steps efficiently coupling coarse and microscopic state spaces. The method can be designed to sample the exact or controlled-error(More)
We propose an efficient Markov Chain Monte Carlo method for sampling equilibrium distributions for stochastic lattice models, capable of handling correctly long and short-range particle interactions. The proposed method is a Metropolistype algorithm with the proposal probability transition matrix based on the coarsegrained approximating measures introduced(More)
We present a new framework for constructing parallel algorithms for lattice Kinetic Monte Carlo (KMC) simulations. These algorithms have the capacity to simulate a wide range of spatio-temporal scales of spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms, while they can be tailored to(More)
information metrics Evangelia Kalligiannaki, a) Vagelis Harmandaris, 2, b) Markos A. Katsoulakis, c) and Petr Plecháč d) Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion, Greece IACM/FORTH GR-71110 Heraklion, Greece Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA 01003, USA Department(More)
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